Considerable attention has been focused on predicting RNA-RNA interaction since it is a key to identifying possible targets of non-coding small RNAs that regulate gene expression post-transcriptionally. A number of computational studies have so far been devoted to predicting joint secondary structures or binding sites under a specific class of interactions.

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Assists users in the prediction of microRNA target. RNAhybrid identifies minimum free energy hybridization of a long (target) and a short (query) RNA. The software was able to predict bona fide targets in Drosophila melanogaster at high specificity. It can be used as a webservice for remote calls from user-implemented programs.

Determines the interactions between two RNA molecules. IntaRNA computes the sum of the free energy of hybridization and the free energy required for making the interaction sites accessible to proceed. It can be applied to non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs). This tool is able to find multiple potential target sites per sRNA and can be used for the prediction of other types of RNA-RNA interactions.

Predicts secondary structures of single stranded RNA or DNA sequences upon dimer formation. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state.

A tool especially created to rapidly search for short interactions between two long RNAs. RNAplex uses a slightly different energy model which reduces the computational time by a factor 10-27 compared to RNAhybrid. In addition a length penalty allows to focus the target search on short highly stable interactions.

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